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An Extensible Model-Based Mediator System with Domain Maps

An Extensible Model-Based Mediator System with Domain Maps. Amarnath Gupta * Bertram Ludäscher * Maryann E. Martone +. * San Diego Supercomputer Center (SDSC) + National Center for Microscopy and Imaging Research (NCMIR) University of California, San Diego (UCSD).

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An Extensible Model-Based Mediator System with Domain Maps

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  1. An Extensible Model-Based Mediator System with Domain Maps Amarnath Gupta* Bertram Ludäscher* Maryann E. Martone+ *San Diego Supercomputer Center (SDSC) +National Center for Microscopy and Imaging Research (NCMIR) University of California, San Diego (UCSD)

  2. Surface atlas, Van Essen Lab stereotaxic atlas LONI  MODEL-BASED Mediation MCell, CNL, Salk CCB, Montana SU NCMIR, UCSD Federation of Brain Data using Model-Based Medition Result (XML/XSLT) PROTLOC Result (VML) ANATOM

  3. ??? Integrated View ??? ??? Integrated View Definition ??? ???Mediator ??? The Need for Semantic Integration Cross-source queries What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity? How about other rodents? Cross-source relationships are modeled Semantic (knowledge-based) mediation services Data, relationships, constraints are modeled (CMs) Wrapper Wrapper Wrapper Wrapper Web protein localization morphometry neurotransmission CaBP, Expasy

  4. Integrated-DTD := XML-QL(Src1-DTD,...) DOMAIN MAP IF  THEN  IF  THEN  IF  THEN  Structural Constraints (DTDs), Parent, Child, Sibling, ... A = (B*|C),D B = ... . . .... .... .... .... (XML) Objects Raw Data Raw Data ConceptualModels Raw Data XML-Based vs. Model-Based Mediation CM ~ {Descr.Logic, ER, UML, RDF/XML(-Schema), …} CM-QL ~ {F-Logic, OIL, DAML, …} Integrated-CM := CM-QL(Src1-CM,...) Logical Domain Constraints No Domain Constraints Classes, Relations, is-a, has-a, ... C1 C2 R C3 XML Elements XML Models

  5. Model-Based Mediation with DOMAIN MAPS (DMs) • “Semantic Road Maps” for situating source data • => navigational aid (browsing source classes at the conceptual level) • => basis for integrated views across multiple worlds • => link points (concepts) and labeled arcs (roles) • => formal semantics (in FL and/or DLs) • Example: ANATOM DM • = antatomical entities (concepts) + is_a, has_a, overlaps, ... (roles) • => from syntactic equality to semantic joins LINK(X,Y): X.zip =Y.zip X.addr in Y.zip X.zip overlaps Y.county ... Integrated-CM(Z1,...) := get X1,... from Src1; get X2,... from Src2; LINK (Xi, Yj); Zj = CM-QL(X1,...,Y1,...)

  6. ANATOM Domain Map

  7. ANATOM Domain Map with Registered Data ANATOM DATA

  8. Integrated View Definition DERIVE protein_distribution(Protein, Organism, Brain_region, Feature_name, Anatom, Value) FROM I:protein_label_image[ proteins ->> {Protein}; organism -> Organism; anatomical_structures ->> {AS:anatomical_structure[name->Anatom]}] , % from PROLAB NAE:neuro_anatomic_entity[name->Anatom; % from ANATOM located_in->>{Brain_region}], AS..segments..features[name->Feature_name; value->Value]. • provided by the domain expert and mediation engineer • declarative language (here: F-logic) Query Processing

  9. PROTLOC-AxioMap Client-Side Result Visualization(using AxioMap Viewer: Ilya Zaslavsky)

  10. FL rule proc. LP rule proc. Model-Based Mediator Prototype USER/Client CM (Integrated View) Domain Map DM Mediator Engine Integrated View Definition IVD XSB Engine Graph proc. GCM GCM GCM CM S1 CM S2 CM S3 CM Plug-In CM Queries & Results (exchanged in XML) Logic API (capabilities) CM-Wrapper CM-Wrapper CM-Wrapper XML-Wrapper XML-Wrapper XML-Wrapper S3 S1 S2

  11. Mediation Services: Semantic Annotation Toolsline drawing =annotate=> (spatial) DB for mediation

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